Allogeneic blood HSCT, whether performed for a malignant or a non-malignant condition, relies on the use of a pre-transplant conditioning regimen. Traditionally, very high doses of chemotherapy or total body irradiation have been utilized as conditioning. The use of intensive conditioning, which, practically speaking eliminates the host marrow and immune system, however, can produce serious and sometimes fatal infections and injuries to vital organs, such as the liver and lung. In children, the use of intensive conditioning can also produce serious late effects, including hypogonadism, stunted growth, impaired cognitive development and secondary malignancies.